Biomedical subjects

Pep Español

Publications and source records attributed to Pep Español.

6 recordsLinked to original sources

PubMed2006

Markovian approximation in a coarse-grained description of atomic systems.

The Markovian assumption stating that memory effects can be neglected is a crucial assumption in the theory of coarse-graining. We investigate the coarse-graining of a one-dimensional chain of oscillators where the atoms are grouped into clusters or blobs. When the interaction between oscillators is through Hookean springs, the cluster dynamics is non-Markovian, as has been recently noted by Cubero and Yaliraki [J. Chem. Phys. 122, 03418 (2005)]. When the oscillators interact through a nonlinear potential of the Lennard-Jones type, the dynamics turns out to be Markovian. The different behavior in both types of interactions is attributed to the persistence of sound waves in the harmonic case, which are strongly suppressed in the nonlinear case.

Journal Article↗

PubMed2005

Smoothed particle hydrodynamics model for phase separating fluid mixtures. I. General equations.

We present a thermodynamically consistent discrete fluid particle model for the simulation of a recently proposed set of hydrodynamic equations for a phase separating van der Waals fluid mixture [P. Español and C.A.P. Thieulot, J. Chem. Phys. 118, 9109 (2003)]. The discrete model is formulated by following a discretization procedure given by the smoothed particle hydrodynamics (SPH) method within the thermodynamically consistent general equation for the nonequilibrium reversible-irreversible coupling (GENERIC) framework. Each fluid particle carries information on the mass, momentum, energy, and the mass fraction of the different components. The discrete model allows one to simulate nonisothermal dynamic evolution of phase separating fluids with surface tension effects while respecting the first and second laws of thermodynamics exactly.

Journal Article↗

PubMed2005

Smoothed particle hydrodynamics model for phase separating fluid mixtures. II. Diffusion in a binary mixture.

A previously formulated smoothed particle hydrodynamics model for a phase separating mixture is tested for the case when viscous processes are negligible and only mass and energy diffusive processes take place. We restrict ourselves to the case of a binary mixture that can exhibit liquid-liquid phase separation. The thermodynamic consistency of the model is assessed and the potential of the model to study complex pattern formation in the presence of various thermal boundaries is illustrated.

Journal Article↗

PubMed2003

Thermodynamically consistent fluid particle model for viscoelastic flows.

A recently proposed viscoelastic dissipative particle dynamics model is put into a thermodynamically consistent form that allows for nonisothermal situations. This model consists of fluid particles that have an additional elastic vector characterizing the state of elongation of the molecules within the fluid particle. Very simple physical mechanisms are proposed for the dynamics of the elastic vector that, with the help of the GENERIC formalism, allows us to derive the full set of dynamic equations for the model. The model is further generalized to include polymer diffusion. The connection of the present model with the CONNFFESSIT approach and the Brownian configuration field approach is discussed.

Computer Simulation↗

PubMed2003

Smoothed dissipative particle dynamics.

We present a fluid particle model that is both a thermodynamically consistent version of smoothed particle hydrodynamics (SPH) and a version of dissipative particle dynamics (DPD), capturing the best of both methods. The model is a discrete version of Navier-Stokes equations, like SPH, and includes thermal fluctuations, like DPD. This model solves some problems with the physical interpretation of the original DPD model.

Journal Article↗

PubMed2002

Coarse graining from coarse-grained descriptions.

We present a generalization of Zwanzig's method of projection operators to the case where the underlying dynamics is not deterministic. The method allows us to perform a coarse graining of an already coarse-grained level of description in which fluctuations are important. The initial level of description is described by a Fokker-Planck equation and, under suitable approximations, the final slower level of description is also described by a Fokker-Planck equation. We illustrate the method for the simple case of the diffusion of colloidal particles at two levels of descriptions.

Colloids↗